Association Analysis of GABRA5, SOX13, and AGL Gene Polymorphisms with Growth Traits in Dongfeng Sika Deer

To investigate the association between polymorphisms in the GABRA5, SOX13, and AGL genes and growth traits in Dongfeng sika deer and to identify potential molecular markers for breeding, this study was conducted based on prior genome-wide association analysis. Based on the previous GWAS analysis of 266 Dongfeng sika deer, the SNP loci of GABRA5, SOX13, and AGL genes were detected in 36 male deer samples. The genetic parameters were calculated, and an association analysis with growth traits was carried out. Phenotypic analysis indicated that body weight and chest circumference had higher coefficients of variation than other growth traits, and body weight showed a strong positive correlation with body-slant length (r = 0.743, p < 0.01) and a moderate correlation with chest circumference (r = 0.709). A total of six SNP loci were identified, including three within GABRA5 (Chr13-8442730, Chr13-9033380, and Chr13-9045819), one within SOX13 (Chr14-5681678), and two within AGL (Chr20-66603370 and Chr20-66618510). The dominant genotypes at these loci include CG (CC), AA, CG, CC (CG), AA, and GG (GC). Linkage disequilibrium analysis revealed a relatively strong association between Chr13-8442730 and Chr13-903380 on chromosome 13. Combined genotype analysis showed that diplotype CCCGGC was associated with higher body weight and larger chest circumference than other genotype combinations. Gene expression analysis showed that the relative expression levels of GABRA5, SOX13, and AGL were lower in the low-growth group than in the high-growth group, and expression variation was also observed within groups. Overall, gene expression levels appeared to be positively associated with growth traits, with higher expression associated with improved growth performance. These findings suggest that GABRA5 and AGL may serve as candidate genes for further investigation and that the identified SNP loci may contribute to the development of molecular markers for the selection of growth traits in Dongfeng sika deer. The results provide a preliminary basis for molecular breeding and genetic improvement strategies in Dongfeng sika deer bucks and serve as an important reference for genetic improvement of growth traits in Cervidae.